tbuckley/cabot-search huggingface dataset:
Abstract 3384: Combined DNA methylation analysis in size based CTC fraction and matched plasma-cfDNA provides prognostic information in early stage NSCLC
Authors: Athina N. Markou, Dora Londra, Victoria Tserpeli, John Kollias, Emilia Tsaroucha, Ioannis Pateras, K Potaris, Ioannis Vamvakaris, Athanasios Kotsakis, Vasilis Georgoulias, Evi Lianidou
Journal: Cancer Research (2022)

Abstract Background: Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) analysis represents a liquid biopsy approach for real-time monitoring of tumor evolution. DNA methylation is considered to be an early event in the process of cancer development and progression. The aim of the present study was to evaluate whether detection of DNA methylation of selected tumour suppressor genes in size-based CTC fraction and matched ctDNA could provide prognostic information in early stage NSCLC. Methods: The methylation status of five selected gene promoters (APC, RASSFIA1, FOXA1, SLFN11, SHOX2) was examined by highly specific and sensitive real time methylation specific PCR assays in: a) a training group of 35 primary tumours and their corresponding adjacent non-cancerous tissues of early stage NSCLC patients, b) a validation group of 22 primary FFPEs tumor tissues and 42 peripheral blood samples of early stage NSCLC patients that gDNA was isolated from FFPEs, sized-based CTCs and plasma, and c) a control group of healthy blood donors (n=12). Results: All five gene promoters tested were highly methylated in the training group of primary tumours; methylation of SHOX2 promoter in the primary tissues was associated with unfavorable outcome. RASSFIA and APC were found methylated in plasma-cfDNA samples at 14.3% and 11.9% respectively, whereas in the corresponding size-based CTC-enriched fractions SLFN11 and APC promoters were methylated in 7.1%. The incidence of relapse was higher in patients with i) promoter methylation of APC and SLFN11 in plasma-cfDNA (P=0.037 and P=0.042 respectively) and ii) at least one gene promoter was methylated in the sized-based CTC fraction or plasma-cfDNA. Conclusions: Although in liquid biopsy components methylation of these gene promoters was significantly lower than in the primary tumors, the combination of DNA methylation analysis in sized-based CTC fraction and plasma-cfDNA revealed clinical relevance. Additional studies are required to validate our findings in a large cohort of early stage NSCLC patients. Citation Format: Athina N. Markou, Dora Londra, Victoria Tserpeli, John Kollias, Emilia Tsaroucha, Ioannis Pateras, K Potaris, Ioannis Vamvakaris, Athanasios Kotsakis, Vasilis Georgoulias, Evi Lianidou. Combined DNA methylation analysis in size based CTC fraction and matched plasma-cfDNA provides prognostic information in early stage NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3384.
Abstract 1687: Cyto R1 Platform enriches samples’ viability for single-cell sequencing and downstream assays
Authors: Alexandra R. Hyler, Alicia M. Cole, Ridi Barua, Amiran K. Dzutsev, Eva M. Schmelz
Journal: Cancer Research (2022)

Abstract Single-cell level investigations such as DNA and RNA sequencing, protein analyses, and phenotypic studies require an input sample with a high rate of viability (&amp;gt;90%). If too many dead cells are present in the input, degraded proteins and ambient DNA or RNA can increase background noise that may lead to missing identification of crucial targets. Since the cost for single-cell sequencing experiments still remains high, it is critical to ensure the input sample is optimized for high viability to ensure cost-effective and reproducible data. Current bead assays or other sample viability enrichment techniques used in preparation for single-cell analyses typically result in a significant sample loss, sometimes sacrificing 80% of the starting sample, and these preparation steps require multiple passes (&amp;gt; 45 minutes time) and costly kits. These beads or kits can be biased and change the cell population, subject cells to unwanted stresses, and diminish sample integrity with the time needed for preparations. Here, we investigate sample cell viability enrichment on the Cyto R1 Platform, a label-free, cell enrichment, sorting, and recovery platform. At the core, the Cyto R1 uses Cyto Chips, microfluidic technologies with electrical fields, to phenotypically enrich and sort various cells based upon cells’ unique physical structures and subcellular features. Thus, the Cyto R1 ensures native cell recovery without any unwanted cell tagging to maximize sample integrity. In this work, a variety of single cell solutions derived from T cell lymphoma tumors, ascites fluid, and organ tissues were enriched for viable cells to obtain a final sample viability over 90%. Additionally, we aimed to achieve a minimum of 50,000 viable cells, a common target for single-cell sequencing, in as rapid a timeframe as possible. In one sample origin tested, murine T cell lymphomas, the average starting viability was 65 ± 6.5%, and the final viability after enrichment on the Cyto R1 Platform was 95.8 ± 1.8%. Similarly, murine ascites cell mixtures were enriched from average viabilities below 55% up to 91.6 ± 4.2%. For all samples tested, &amp;gt;50,000 viable cells were obtained in under 30 minutes. This work demonstrates that the Cyto R1 can effectively and efficiently enrich a variety of starting samples for high viability (&amp;gt;90%) as required for downstream assays and single-cell sequencing. Citation Format: Alexandra R. Hyler, Alicia M. Cole, Ridi Barua, Amiran K. Dzutsev, Eva M. Schmelz. Cyto R1 Platform enriches samples’ viability for single-cell sequencing and downstream assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1687.
Abstract LB096: EGFR-dependent inflammation as a driver of breast cancer
Authors: Angelica Escoto
Journal: Cancer Research (2022)

Abstract Triple Negative Breast Cancer (TNBC) is one of the most aggressive and metastatic subtypes of hormone receptor negative breast cancers. Evidence supports that most patients with TNBC overexpress the Epidermal Growth Factor Receptor (EGFR), yet its role in driving the disease remains unclear. Therapies have been developed to target EGFR, but EGFR-targeted antibodies and tyrosine kinase inhibitors fail to work effectively in breast cancer patients. A possible explanation is that in addition to its canonical function at the membrane, EGFR has a non-canonical function where it can undergo retrograde trafficking to the nucleus, making it resistant to antibody-based therapeutics. Once in the nucleus, EGFR is known to function as a transcriptional cofactor for STAT3, STAT5, and E2F1, thereby regulating the expression of genes that promote inflammation and cell proliferation. Via RNA-Seq analysis, we demonstrate that EGFR can regulate different subsets of genes depending on its canonical signaling activity or nuclear role. Our goal is to understand and distinguish this difference in regulation to assess how EGFR affects inflammation. We hypothesize that EGFR is modifying inflammation differently depending on its canonical or non-canonical role, thereby driving disease progression in multiple ways. We have found that canonical EGFR can induce interleukin 8 while nuclear EGFR can repress interleukin 6 through the use of either kinase inhibitors (IL8) or blocking nuclear translocation of EGFR (IL6). Correlated with these changes are alterations in growth and inflammatory profiles in both a triple negative inflammatory mouse model and an EGFR-driven breast cancer mouse model. We are now investigating the role of nuclear-EGFR-dependent inflammation in driving tumor progression. Understanding the different mechanisms by which EGFR modifies inflammation and the tumor microenvironment would allow us to develop more specific targets for patients with TNBC. Citation Format: Angelica Escoto. EGFR-dependent inflammation as a driver of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB096.
Abstract 5764: Genomic profiling of cutaneous, acral and mucosal melanomas in Chinese populations
Authors: Jing Chen, Ting Ye, Li Fan, Jieying Zhang, Rubo Cao, Yanshen Liu
Journal: Cancer Research (2022)

Abstract Background: Targeted therapies and immunotherapies have significantly improved the survival of patients with cutaneous melanoma. Nevertheless, patients with acral and mucosal melanomas show limited benefit. The proportion of acral and mucosal subtypes are much higher in Chinese populations than Caucasians. Therefore, it is of great interest to detail the genomic features of acral and mucosal melanomas and compare these with cutaneous melanoma. Methods: A total of 111 Chinese patients with melanoma treated in Union Hospital, Tongji Medical College, Huazhong University of Science and Technology were enrolled in this study, comprising 32 cutaneous(28.8%), 41 acral(36.9%) and 26 mucosal(23.4%) subtypes. NGS-based genomic profiling of major cancer-related genes was performed on formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens with matched blood samples. Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous missense mutations. Results: The most commonly mutated genes of cutaneous melanoma include BRAF(48%), CDKN2A(41%), CDKN2B(41%), NRAS(22%) and PTEN(22%). In acral melanoma patients, the mutation rate of BRAF was 10% while NRAS(31%), CDKN2A(21%), EMSY(21%), KIT(18%), CCND1(18%)) and NF1(18%) were frequently mutated. Mucosal melanomas were found most commonly to have mutations in CDKN2A(36%), KIT(32%), CDKN2B(28%), PDGFRA(24%), KDR(20%) and BRAF(16%). In acral and mucosal subtypes, the overall mutation rates of BRAF were significantly lower while the relative proportions of non-V600 mutations were higher as compared to cutaneous subtype. These may explain the less significant survival benefit of BRAFi+/-MEKi in acral and mucosal melanomas. In contrast, KIT mutations including SNVs and amplification, were enriched in acral and mucosal melanomas. Acral melanomas had lower mutation load than mucosal melanomas(2.42 Muts/Mb vs 4.84 Muts/Mb, p=0.0002), while cutaneous melanomas(4.03 Muts/Mb) did not differ from other subtypes in mutation burden. Additionally, patients with TERT, APC and FAT1 gene mutations had a significantly higher TMB than patients with wild-type genes respectively, indicating more activated anti-tumor immune profiles and suggesting therapeutic benefit from immune checkpoint inhibitors. Conclusions: We conducted a direction comparison of comprehensive genomic profiles of different melanoma subtypes among Chinese patients. The genomic alterations identified in our study may provide reference to discover potential strategies for targeted therapy and immunotherapy in acral and mucosal melanomas. Citation Format: Jing Chen, Ting Ye, Li Fan, Jieying Zhang, Rubo Cao, Yanshen Liu. Genomic profiling of cutaneous, acral and mucosal melanomas in Chinese populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5764.
Abstract 1582: Chloroquine inhibites Rab11 mediated E-cadherin transport in collective colon cancer cell migration
Authors: Xiang-Ling Hou, Hui Min Koo, Yu-Cheng Weng, Yi-Wen Lu, Viriya Adhiguna Winarso, Yu-Lin Li, Wei-Ting Chao
Journal: Cancer Research (2022)

Abstract Cell migration is regulated by multiple molecular pathways to change the morphology from epithelial to mesenchymal type and is important in cancer metastasis. In has been demonstrated epithelial mesenchymal transition (EMT) is related to E-cadherin expression level. The loss of E-cadherin expression results in tumor proliferation and metastasis. Recently, studies have been demonstrated the collective cancer cell migration which expresses high E-cadherin is a powerful mechanism of metastasis. Therefore, the role of E-cadherin in cancer metastasis is still not clear. Clathrin-mediated endocytosis (CME) was shown to regulate E-cadherin turnover on the membrane and the function of lysosome is also associated with cell vesicle trafficking, however, the role of lysosome in collective cell migration is not known. This study is investigating the role of lysosome in regulating E-cadherin dynamics through vesicle trafficking in collective colon cell migration. In the experiment, we used colon cancer cells with epithelial morphology and observed the relation of E-cadherin with endocytic protein clathrin, Rab5 and the recycling protein Rab11 in collective migrated cells. In the result, inhibition of lysosome activity by chloroquine treatment has great suppression effect on anchorage independent cell growth and inhibited collective cell migration. We observed that nocodazole treatment inhibited clathrin-mediated endocytosis, which caused E-cadherin to accumulate on the cell membrane. Western blot and confocal microscopy demonstrated chloroquine treatment induced Rab11 expression and accumulated in the cytosol which affected E-cadherin turnover. Our results demonstrated inhibits lysosome activity can suppress colon cancer cell growth and collective migration through lysosome mediated E-cadherin translocation. Chloroquine may be the potential treatment for colon cancer therapy. keywords: colon cancer, collective cell migration, E-cadherin, vesicle trafficking, lysosome Citation Format: Xiang-Ling Hou, Hui Min Koo, Yu-Cheng Weng, Yi-Wen Lu, Viriya Adhiguna Winarso, Yu-Lin Li, Wei-Ting Chao. Chloroquine inhibites Rab11 mediated E-cadherin transport in collective colon cancer cell migration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1582.
Abstract 268: Role of aquaporins in mechanotransduction and extracellular vesicle-mediated cancer cell communication in complex physical microenvironments
Authors: Ian Smith, Allison Moses, Stephanie Kronstadt, Steven Jay, Kimberly Stroka
Journal: Cancer Research (2022)

Abstract Introduction: Metastasis is driven by the migration of cancer cells to different areas of the body, but the mechanisms that induce cell movement are still poorly understood. Aquaporins (AQPs), transmembrane water transport proteins, have been linked to tumor growth, metastasis, and more invasive phenotypes. However, the exact mechanisms behind AQP dysregulation and its role in mediating cancer migration remain unknown. Physical cues and extracellular signals from the tumor microenvironment have been implicated in the progression of cancer; yet the role AQPs play in sensing and signaling have yet to be elucidated. Recent studies have shown the paracrine signaling within the tumor microenvironment is mediated in part by cell secreted extracellular vesicles (EVs). EVs are membrane-delimited nanoparticles capable of protecting and transporting protein and nucleic acid cargo for intercellular communication. EV mediated paracrine signaling has been shown to participate in various steps of tumor progression. Cells are also able to sense complex mechanical signals from the tumor microenvironment to direct more invasive cellular responses. Understanding the role AQPs play in sensing and signaling within the tumor microenvironment can provide a more holistic view of the way AQPs influence cancer progression. Materials and Methods: To study the role of AQP containing EVs and AQPs influence on mechanotransduction to facilitate cancer cell migration, this study has employed 3D in vitro models, including microfluidic devices, to recapitulate relevant in vivo conditions in concert with confocal microscopy to understand cell behaviors. EVs were isolated via tangential flow filtration. AQP levels were down regulated with siRNA complex or upregulated via AQP5-GFP plasmids. Results: Knocking down AQPs with siRNAs, confirmed with western blotting, was shown to reduce cellular migration on 2D surfaces and in confining microenvironments. We have also found that AQPs can enhance the integrin mediated mechanotransduction pathway, which has been implicated in cell proliferation and migration. Effects of integrin mediated mechanotransduction were reversed by suppressing AQP expression. Finally, we have made the exciting discovery that cancer cells secrete extracellular vesicles that contain AQPs. These EVs could be released into the tumor microenvironment to enhance tumor migration. Further work is being conducted to elucidate the AQP-EV relationship. Citation Format: Ian Smith, Allison Moses, Stephanie Kronstadt, Steven Jay, Kimberly Stroka. Role of aquaporins in mechanotransduction and extracellular vesicle-mediated cancer cell communication in complex physical microenvironments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 268.
Abstract 2274: Identification of predisposition and progression gastric cancer biomarkers in Latinos
Authors: Ana Patricia Estrada-Florez, Paul Lott, Ted Toal, Nicole Halmai, Elizabeth Quino, Alma Poceros-Coba, Alix Guevara, Fabian Castro, Jhon Suarez, John Mcpherson, Rasika Venkatesh, Hongyong Zhang, Apri Vang, Guadalupe Polanco, Joana Guerra, Graciela Molina, Carol Parra, Adriana Della Valle, Esteban Castelao, Manuel Teixeira, Mabel Bohorquez, Javier Torres, Alejandro Carvajal Corvalan, Luis G. Carvajal-Carmona
Journal: Cancer Research (2022)

Abstract Gastric cancer (GC) disproportionally affects people of Latino ancestry and represent a leading cause of incidence and mortality disparities in this minority populations. When compared to Non-Latino Whites, Latinos are ~2-fold more likely to be diagnosed with and to die of GC. The goal of our research program is to contribute to GC research in patients of Latino ancestry and advance cancer health disparity research. One of the research projects aims at identifying germline variants associated with GC risk. To do so, we are identifying novel gastric cancer genes and detecting mutations in previously reported GC genes, using whole-exome sequencing, in 500 patients who have been diagnosed with early-onset GC and/or who had GC and family history of cancer. Whole exome sequence data collection was recently completed and is being analyzed with the primary goals of estimating the prevalence and penetrance in known cancer genes as well as the identification of new GC genes. Using in-house exome data and publicly available genetic data, we will identify variants with predicted impact in the phenotype to design a panel that will be used for their detection in gastric preneoplasia biopsies. These variants will be tested using duplex sequencing, a highly sensitive method that can detect very rare mutations with ultra-depth sequencing. We will then select the variants with likely functional consequences for tumor initiation and/or progression to generate isogenic gastric organoids to investigate their effect in proliferation, differentiation, and gene expression. We aim to generate a body of work that can be used for risk assessment, prevention, early diagnostic, and that will lead to better outcomes for GC in this important U.S. minority. Dr. Ana Estrada-Florez is the recipient of the AACR Cancer Health Disparities Fellowship. Citation Format: Ana Patricia Estrada-Florez, Paul Lott, Ted Toal, Nicole Halmai, Elizabeth Quino, Alma Poceros-Coba, Alix Guevara, Fabian Castro, Jhon Suarez, John Mcpherson, Rasika Venkatesh, Hongyong Zhang, Apri Vang, Guadalupe Polanco, Joana Guerra, Graciela Molina, Carol Parra, Adriana Della Valle, Esteban Castelao, Manuel Teixeira, Mabel Bohorquez, Javier Torres, Alejandro Carvajal Corvalan, Luis G. Carvajal-Carmona. Identification of predisposition and progression gastric cancer biomarkers in Latinos [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2274.
Abstract 2250: Eosinophil-to-lymphocyte ratio and cancer risk in the UK Biobank
Authors: Jeanny Wang, Eric Engels, Minkyo Song
Journal: Cancer Research (2022)

Abstract Background: Eosinophils exhibit anti-tumor cytotoxic responses in the tumor microenvironment. Some atopic diseases, characterized by elevated peripheral eosinophils, are inversely associated with cancer risk. The balance of atopy and immunity may be estimated by an eosinophil-to-lymphocyte ratio (ELR). This study aims to understand the role of ELR as a biomarker in carcinogenesis. Methods: We evaluated 445,404 adults aged 37-73 years at baseline in a prospective cohort study, the UK Biobank, who were cancer-free at initial assessment, had more than one year of follow-up, and had baseline white blood cell (WBC) count and differential measurements. ELR was categorized into quartiles. Incident cancers were ascertained from cancer registries from 2006-2015. Multivariable Cox regression was used to estimate per quartile ELR hazard ratios (aHRs) separately for 52 cancer sites, adjusted for age (quartiles), sex, race (white, non-white), smoking/alcohol (never, past, current), body mass index (&amp;lt;25, 25-30, ≥30 kg/m2) and total WBC (quartiles). Multiple comparisons were considered by a Bonferroni-corrected threshold (p&amp;lt;0.00096). Results: Over a median follow-up time of 6.9 years from baseline, 22,853 incident cancers were diagnosed. The median ELR was 0.07 (interquartile range=0.05-0.12). Higher ELR was inversely associated with overall cancer risk (aHR 0.98, 95%CI: 0.97-0.99; p-trend=0.0001) and chronic lymphocytic leukemia (0.50, 0.44-0.56; &amp;lt;0.0001). We also observed suggestive inverse ELR associations with other lymphocytic leukemia, acute and other myeloid leukemia, myeloma, melanoma and cancers of the nose/middle ear, tongue, prostate (aHR range: 0.63-0.97; p-trend&amp;lt;0.05). Per quartile increase of ELR was suggestively associated with increased risk of diffuse large B-cell lymphoma (aHR 1.13, 95%CI: 1.03-1.25; p-trend=0.01). Conclusion: We observed inverse associations between ELR and cancer risk in a large general population. Our findings suggest that atopy may be protective against cancer. Future research is warranted to elucidate the relationship between atopy and immunity in tumor surveillance. Impact/Significance: ELR presents a cost-effective and routinely accessible biomarker that may have implications for carcinogenesis, and may be leveraged to inform early detection of certain cancers. Citation Format: Jeanny Wang, Eric Engels, Minkyo Song. Eosinophil-to-lymphocyte ratio and cancer risk in the UK Biobank [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2250.